Metroid: Regeneration
by Manof1000Words
Summary: Set after Metroid Fusion, Samus Aran embarks on a new mission to put a halt to the Pirate's new Phazon hoarding scheme with the help of a rookie bounty hunter. NEW BEGINNING! Please Read and Review!
1. The Task

Metroid: Regeneration

Chapter 1: The Task

Board room 7-A was on of the smaller board rooms at Galactic Federation's Nahr'kayneea Outpost. It was only able to seat eight. Since there were seven generals at Nahr'kayneea, Samus figured that this meeting she was about to attend was to be between her and the generals of the outpost. The room's walls were covered in white panels, and in the middle was a large, white, conference table surrounded by large white office chairs. Shortly after Samus's arrival to the board room, the generals filed in. The last was General Orlow.

"This is not a formal meeting," said General Orlow, "but more of a debriefing of Samus's mission to investigate space pirate operations on the planet Otocon. For those who are unaware, she arrived only an hour ago, and I believe she has some interesting news for us, since in the past Samus has been most successful in retrieving inside information from the space pirates' operations. I call forth Samus Aran."

"Thank you, General Orlow." Samus, who was seated next to General Orlow, stood up and moved to the front of the room. "I realize my adventures on Otocon caused great controversy, and I still think the honorable General Orlow rejects the idea despite the fact that I have returned in one piece. But I have some rather disturbing news. Upon further investigation of the space pirates' Otocon operations, I discovered that the space pirates are once again hoarding phazon. The Otocon base was equipped with large phazon storage units and equipment used to manipulate the gathered phazon.

"Now, even though I was unable to discover why they are hoarding phazon, I feel something dangerous is looming over our horizon. They have already recreated elite pirates by fusing the phazon with some of their own. If they persist with their phazon research, they may recreate the Omega Pirate. But not only one. If my calculations are correct, they already have enough phazon to create an army of elite pirates, or a small squad of omega pirates. If this were to happen, the space pirates would have the Galactic Federation on their knees begging for mercy; mercy the space pirates would not provide."

General Hallman, from sector D, looked worried. "But that could mean…"

"…The utter annihilation of the Galactic Federation," replied Samus. "This would mean the entire galaxy would fall under control of the space pirates."

"THE SPACE PIRATES MUST BE STOPPED!" yelled General Jack from sector O, slamming his fists on the conference table. This made General Hallman jump.

"Calm down General Jack," General Orlow said, soothingly. That is what this meeting is for; to listen to Samus's report and to devise a plan of action."

The general from sector Q, General Mandate, raised his hand. "May I make a suggestion?"

"Of course, General Mandate, that is why we're here," said General Orlow.

"Well, if the space pirates are hoarding phazon then I suggest we send someone to, what planet was it? Oh yes, Tallon IV. We should send someone to Tallon IV."

"What would that accomplish?" objected General Jack.

"Well, Tallon IV is a major source of phazon ever since the meteor impacted with that planet a while back. So, one can make the conclusion the space pirates returned operations to Tallon IV to retrieve said phazon. In that case, if we can put a stop to the mining of the phazon on the surface of Tallon IV, it will stop the shipment of phazon to Otocon."

"Possibly stopping the space pirates' evil designs," concluded General Orlow. "That is what we shall do. Samus knows Tallon IV very well, so she is the we shall send. Do you understand your mission Samus?"

"Yes, General Orlow. I understand it completely," Samus replied.

"Good. It has come to my knowledge the chozo have returned to Tallon IV and rebuilt a great city. Perhaps they may have some information for you, Samus Aran."

"Yes, General." Samus left the board room.


	2. New Chozodia

Metroid: Regeneration

Chapter 5: New Chozodia

Nearly a month had passed since the board room meeting at Nahr'Kayneea Outpost and already Samus's jump ship was approaching Tallon IV. The large orange planet slowly crept up on Samus as she finally felt the nostalgia taking its toll. A while back, before SR388 was destroyed, she had come to this planet in pursuit of the space pirates, and found a wrecked space frigate, belonging to the pirates. When Tallon IV came into view, images of lush green jungles, arid deserts of sand and ice, and maze-like caverns bombarded her mind.

Samus entered the atmosphere of Tallon IV and slowly brought the ship in to land. She looked out the window of her ship and surely enough it was raining, as it always did on the Tallon Overworld. And because of it, the grass was a deep, dark, green and the creek was refreshingly blue. But there was something there Samus did not prepare for. There were many miniature chozo running and playing. This struck her as odd since the last time she was here, this place was desolate and dangerous.

"These are our children," said a voice. Samus quickly turned, arm cannon pointing at whoever was behind her. "Don't be startled Samus, we won't hurt you." It was a chozo dressed in a large brown and red robe, typical chozo garb. "Allow me to introduce myself. I am Goldensteen. A resident of New Chozodia."

"New Chozodia?" asked Samus. "Is that what you call this place?"

"No, this is still the Tallon Overworld. New Chozodia is simply the city we chozo constructed upon our return to Tallon IV," Goldensteen replied, smartly. "But I trust someone as yourself does not come to a place like Tallon IV for rest and relaxation, and your true intentions are much more confidential and, perhaps even controversial. We shall go to my humble abode within the city. Come."

Goldensteen turned and brushed aside some vines hanging over the edge of a cliff to reveal a door that Samus had never seen before. The construction of this door was unlike any door upon Tallon IV. She assumed this was the entrance to New Chozodia. On the other side was just a long tunnel that constantly wound downwards, seemingly endlessly. But, as all things, the tunnel did end with another door which opened as Goldensteen approached it. Beyond the door was an enormously large cavern filled with what Samus first thought were large ice spires, but upon closer inspection, she noticed that they were buildings constructed by the chozo.

"Welcome to New Chozodia!" Goldensteen announced, "The only chozo city that I know of which is built entirely underground."

"Its name sure is resonant," Samus noted, bluntly.

"There were two names being considered for this settlement. One was The Underground, the other name was New Chozodia. The latter was chosen in honor of those who have died during the Raid of Zebes and the destruction of old Chozodia." Goldensteen bowed his head and remained silent for about thirty seconds before saying, "My home is just through this corridor."

Goldensteen led Samus through a skinny rock corridor lined with glowing orbs seemingly attached to the walls for lighting. On their way through the tunnel, they past many other chozo continuing with their daily lives, all of them staring at Samus. It's not every day a bounty hunter wearing chozo-made armor walks through New Chozodia. Some of the chozo were heard saying, "It's about time someone arrived to help us!" or, "Finally, those lazy bird-brains on city council are doing something useful for once!" It became obvious to Samus something was happening against the wishes of the chozo. Hopefully, for the sake of Samus's purpose, it meant space pirates.

"This is my home." Goldensteen pointed to a door in the rock wall. Beside the door were chozo runes which roughly translated to 'Apartment 15, Cavern 5'.


	3. Goldensteen and the Story of New Chozodi...

Metroid: Regeneration

Chapter 6: Goldensteen and the Story of New Chozodia

The interior of Goldensteen's New Chozodia apartment was carefully carved out of the rock and the walls smoothed, like those of the Chozo Ruins. He had obviously made a few homey touches by adding the usual chozo furniture, including the table which Samus and Goldensteen both sat.

"Now, Samus, I have some questions for you, but I must ask, do you have any for me?" Goldensteen began.

"Yes, I have many," replied Samus. "But first, I must quench my curiosity. When did the chozo return to Tallon IV?"

"Oh, not too long ago. Actually, the plans for this establishment first began to formulate shortly after the chozo's first arrival. But, unfortunately, the meteor struck, marking the coming of the Great Poison, or phazon, as you know it." Goldensteen sat back in his chair.

"If the phazon caused the original evacuation, is the phazon supply on Tallon IV depleted?" Samus was slightly worried that her trip to Tallon IV would soon be rendered useless and a waste of time.

"No, no, of course not! The presence of the phazon gave us chozo an interesting challenge; we had to find some way to control the phazon. And we found the answer. The plans for a phazon storage unit was made. The unit was then constructed and tested, successfully, too!"

"So there is a phazon storage unit here in New Chozodia?"

"Yes. Many actually. They are what made the building of New Chozodia possible. When excavation began for this underground city, the construction crew came across many phazon deposits, which were extracted and stored in the temporary storage units they had nearby. Upon completion of New Chozodia, permanent storage units were built in the city core and the phazon was transferred from the temporary units to the permanent units."

"The whole process seems to be quite taxing, if you ask me," Samus said, rather bluntly.

"No doubt. In fact, the city coffers were virtually empty. Now, us chozo do not believe in the material, but sadly, the universe revolves around it. To be able to survive, one must have the money. So, the future of New Chozodia seemed dim. That was until someone else took interests into our inventions. The space pirates. They soon sent some ambassadors to New Chozodia and said they wanted to buy the plans to our phazon storage units. But, knowing the space pirates, we turned them down.

"Did they return?" asked Samus, with renewed interest.

"Thrice they did. And upon the third visit, they not only made an offer so magnificent that we could not refuse, they threatened to start a war."

"That's the pirates for ya'."

"Yes, well, the deal was signed. But then the chancellor did something uncalled for. He offered our other device to help with the phazon problem. The P.M.E. Phazon Manipulation Equipment. For this, the space pirates offered twice as much as the storage units. Believe me, the chancellor was swiftly revoked of his title."

Samus laughed. "Shows him to do a deal, undiscussed with the council, especially with the space pirates. But this whole deal with the space pirates in the first place discomforts me greatly."

"I know, Samus, but we were desparate. New Chozodia was on the verge of collapse."

"Yes, I understand that. But the space pirates have launched forth with a scheme to hoard phazon, and they are using your equipment to do it."

"How do you know this?"

"I saw their Otocon headquarters. The worst part is, they have already began to recreate elite pirates. Soon, they will undoubtedly recreate not just one, but many omega pirates. The whole galaxy is in grave danger . . . again."

"I feared something grave, but something as grave as this, I could not imagine. That explains the space pirates' return to Phendrana Drifts and the Phazon Mines."

"So they have, indeed, returned; resuming operations."

"I assume so. Why else would they come to a place like this?" said Goldensteen, still bewildered by the sheer magnitude of it all.

"Look, Tallon IV is the galaxy's largest and only source of phazon. If I can put a stop to the space pirate operations here, operations all over the galaxy would also have to quit."

"What if they rebuild?"

"I deal with that when we get there. But you know what I have to do, can you help me?"

"Yes, I believe I can. I have spent many days exploring the surface of Tallon IV, and I may have come across some passages that you have not." Goldensteen stood up and made his way for the door. "First, we must go to the city core. They may have some equipment we can use. Then, we leave for the Chozo Ruins."

"Chozo Ruins? If my memory serves me correct, we can get to Magmoor Caverns from the Tallon Overworld." Samus stood and followed Goldensteen.

"You can do that, but think about what you propose. The Magmoor entrance to Phendrana is the front door of your rival's lair. It will undoubtedly be heavily guarded. I have discovered in the far reaches of the Chozo Ruins an elevator which leads to the far reaches of Phendrana. From which point we can attack the space pirate research facility from behind. What would you rather do?" Goldensteen said, mockingly.

"Lets go with your plan, Goldensteen."

"Like I said, I have explored this planet to great extent. Trust me with the directions, and I trust you in battle." Both Goldensteen and Samus left the apartment for the city core.


	4. New Acquaintances

Author's Note: You must understand that I consider Samus to be a part of an organization of bounty hunters called the Galactic Alliance of Bounty Hunters. Whether this is the case or not, that is how it will be for this story.

* * *

Metroid: Regeneration

Chapter 7: New Acquaintances

The City Core was a sight to behold. It was not a large network of caverns like the rest of the city, but instead seemed like a large hollowed out mountain. Within this underground bubble, towers were built out of glass and polished marble; the tallest tower being the Galactic and Planetary Affairs building in the middle of the city core.

Samus and Goldensteen were making their way to the Planetary Division of the Galactic and Planetary Affairs building, were Goldensteen's close friend, Ordenstantz, worked. Ordenstantz was sitting at his desk in a small office just next to the reception area of the Planetary Division. His office was completely white, as was the rest of the Planetary Division.

"You chozo sure do have an interesting décor motif going on here," Samus noted as she took the whiteness of her surroundings.

"The white color scheme is meant to represent the purity of the chozo and their presence of Tallon IV. But I must talk with Ordenstantz, you can continue on ahead and repair or replace some of your gear. You might meet somebody you know." Goldensteen pointed to a set of large, white, double doors with a sign above it reading, "The Hub: Lab A".

_Well, 'The Hub' must be a very common name!_ Samus said to herself. She walked through the door and entered a room buzzing with activity. Chozo were everywhere; more than Samus has ever seen in one room at a time, including the City Core. But one thing caught her eye. A suit; a brand new suit unlike anything she has seen the chozo build before. The design was very un-chozo. When Samus approached, the suit turned to look at her and the accompanying chozo began to speak.

"Ah, Samus Aran! I trust you were also sent here by the Galactic Alliance of Bounty Hunters as well," said the chozo.

"Actually no; I was sent here by the Galactic Federation," Samus said, eying the person in the suit. "Who is this?"

"I'm surprised you haven't met yet. He is from the Galactic Alliance, like yourself. And I hear he is quite the bounty hunter. His name is…"

"…Mada Edoc," the mysterious bounty hunter said. Samus examined his suit; there was something oddly familiar about it. Then it struck her.

"That suit… it is space pirate technology, isn't it?" Samus asked carefully.

"Yes, that is right. Got it when I was in the Yontiss system. Nasty little buggers those pirates are, but I was able to get into their base, steal some data, and then I built this suit myself. So there are a few things that are space pirate technology," Mada said, admiring his own armor. "Yours is of chozo technology I believe."

"Yes, it is. The difference between my suit and yours is mine was not stolen. The chozo gave it to me when they took me in."

"What do you mean by 'took you in'?" Mada was confused.

"When my parents were killed by space pirates, the chozo raised me as their own. My basic gear is chozo technology."

"You must really hate space pirates, then, don't you?"

"The sooner they are all eliminated, the better." Samus turned to the chozo. "I need to replace my grapple beam and my gravity boost. Do you have any?"

The chozo's face was no longer as bright as when Samus first met him. "I'm sorry Samus, but we gave away our last grapple beam and gravity boost this morning. But I can get Ordenstantz to order they be built."

"Good. When it's done, send me a transmission. You may have to relay the message from my ship to me."

"Then I will order your grapple beam and gravity boost be made right away." The chozo left through the door Samus had come through.

Samus was still unsure about this bounty hunter before her. Mada seemed to be authentic, he even had the mark of the bounty hunter on his suit. His black and red suit was a strange cross between Samus's phazon infused suit when she was last on Tallon IV, and the suits worn by the space pirates.

"Tell me, Mada. How long have you been a part of the Alliance?"

"Only about a year or so," Mada replied, smugly.

That seemed to check out with Samus. She had not been to Alliance headquarters in a few years. There are probably many new recruits she has not yet met. At that moment, Goldensteen entered.

"Samus, Ordenstantz told me the space pirates have resumed operations in Phendrana and the Phazon Mines. Apparently, the apparatus that we sold them is being used to ship the phazon to Otocon, after it was collected from the Phazon Mines."

"Then all that's left to do is go to Magmoor." Samus was about to leave.

"No. That route is too dangerous. The pirates will undoubtedly have that entrance protected, as well as the link to the Tallon Overworld."

"The how will we get to Phendrana?" Samus asked.

"I my years here, I have been in the Chozo ruins many times and have discovered some secret passages that you have never seen before. You will use these passages to make your way to the Phazon Mines. From there, we must hope the space pirates have built a connection to Phendrana to ship the phazon more discreetly."

"So, you are going after the pirates are you?" Mada asked.

"Yes. They are creating and army that has the ability to destroy every living being in the galaxy." Samus turned to leave.

"I will come with you." Mada picked up a large gun of the table beside him. He slipped it on over his hand and locked it to his arm. "It's and adaptation of your arm cannon, Samus. The difference is I can remove mine and lock it back in place when I need it. It works independently from my suit."

"Fine, but you had better keep up."

Samus, Goldensteen, and Mada Edoc left.


	5. Into the Depths

Author's Note: I apologize for the extended amount of time before this installment. I was in a slight writer's block in both my stories "Regeneration" and "Paper Mario Corrupted". Hopefully, the next chapter will be up sooner.

* * *

Metroid: Regeneration

Chapter 8: Into the Depths

The Chozo Ruins were not as Samus had remembered them. It used to be barren and desolate, but now, it was a hive of activity. Chozos were everywhere. Not just adult chozo, but also children were running around and playing. Before, the Chozo Ruins was a very hostile place where Samus faced many hardships as she tried to rid the ruins of the poison contaminating the waters -- the source being a monster known as the Flaaghra; a monster that lived in a giant plant; a monster that gained its energy from the sun.

"What are all these chozo doing here, Goldensteen?" asked Samus.

"They come here to escape the hustle and bustle of New Chozodia," Goldensteen replied. "It is actually a very popular place for families. The children run through the caverns and the parents follow mainly to be sure the little ones don't get into trouble. Only certain areas of the Ruins have been cleared for public access."

"Why are only certain area cleared for access?"

"Well, there have been numerous sightings of chozo ghosts but they have all been in the areas beyond the Arboretum on the one side and beyond the Magmoor Transport on the other."

"So the spirits of the last chozo inhabitants are still here."

"I'm sorry for interrupting your little history lesson Goldensteen, but where exactly are we going?" Mada said.

"We are heading for the hidden access to the Phazon Mines through the Sun Chamber." Goldensteen noticed Samus searching her logbook as they exited the Main Compound. "This access point is new to you Samus so you have no record of it in your data banks. The only chozo absolutely sure of its location is Ordenstantz."

"Then how are we supposed to find it?" There was a hint of urgency in Mada's voice.

"Don't worry Mada, Ordenstantz gave me the coordinates before we left the City Core."

The three made their way past the mecha-hive and the Magmoor Transport, just where Goldensteen that no one was to travel.

"Goldensteen, I thought you said access to the caverns beyond the Magmoor Transport was restricted?" Mada pointed out.

"I did say so. But some still do travel beyond. Mostly adolescent chozo looking for an adventure. Trust me, the chozo ghosts keep them on their feet." Goldensteen glanced over to Samus who was just wandering alongside minding her business. "We are an exception, Mada. We are on special, secret business."

"Yes, and a chozo general passing through the ruins with two bounty hunters isn't suspicious," Mada mocked. Goldensteen just ignored the comment.

They arrived at the entrance to the Sun Chamber where the Flaaghra once flourished and poisoned the waters of the ruins. Samus remembered the ciricular room all too well. She could see everything as it happened some many years earlier. The giant worm-like creature growing out the center of a flower and her rolling around in morph ball to dodge the fiend's attacks; it was a fearsome fight. But now, the room lay empty, with only a large gaping hole where the Flaaghra once rested.

"That is where we are going," Goldensteen pointed at the giant hole, "into the Flaaghra Caverns."

"When did this happen?" Samus referred to the area that was unexplored to her.

"We excavated what was left of the Flaaghra, the giant flower, and found that its roots created a network of tunnels that lead to the true source of the poison."

Samus felt a chill up her spine.

"Did you feel that?" Mada asked.

"I'm glad to see I'm not the only one," replied Samus.

"It's the silent pass of a chozo ghost," Goldensteen explained. "They remember you, Samus, as an enemy. And you, Mada, are not chozo. They will undoubtedly attack you as well."

Samus switched to her x-ray visor. The room's grayscale came into view, and Samus saw the ghosts. Three of them. All charging their attacks.

"JUMP!" Samus shouted as she jumped of the ledge they were standing on. Mada could not see what was going on for he did not have an x-ray visor, but did as Samus told.

"How do I fight something I cannot see?" Mada was running around the hole, trying to make himself a hard target. The moans of the dead chozo were everywhere.

"They will show themselves eventually! Believe me; they can be beaten without an x-ray visor!" Samus said shooting continuous power blasts at what appeared to be nothing to Mada. But something was definitely there. The blasts would just stop and explode in mid-flight as it hit a chozo ghost.

Samus continued to fight the chozo ghosts and could not help but let a smile come to her face as she saw Mada running around in circles.

"Hey, Mada! There's a ghost on your tail!"

Mada turned around and started firing. Surely enough, his blasts were hitting something that became visible with each concussive hit. Out of a mixture of bravery and pure fear, he continued shooting until his blasts hit the wall. A piercing shriek echoed through the halls of the ruins.

"Is it dead?" Mada yelled over to Samus.

Samus glanced in Mada's direction and saw the spirit burn.

"Yeah." Samus rolled up into her morph ball and rolled towards Mada, thinking they could accomplish more by sticking together. When she reached Mada, she came out of her morph ball. The sight she then saw was amazing, but terrible. Chozo ghosts were floating through the chamber's walls, continuously multiplying. What once was three, was now a hundred, and growing.

"Mada! The ghosts are multiplying! We must get Goldensteen and head into the Flaaghra Caverns!" Samus yelled amongst the moans and groans of the floating specters. Mada acknowledged that he heard and he dashed around the pit to Goldensteen, who was still standing on the ledge.

"Goldensteen! There are too many!" The ghosts made themselves visible for a split second. Goldensteen's eyes grew in sheer horror. "We need to get through the Flaagrha Caverns, now!"

Goldensteen jumped down form his perch and ran for the pit, closely followed by Samus and Mada. They just ran as fast as they could, with Samus glancing back to see if they were followed. The entrance of the tunnel was completely blocked by the racing chozo ghosts.

"Goldensteen, they are still following us! I suggest we find this transport of yours quickly!" Samus said.

"Don't worry Samus, the transport should be just down this tunnel." Goldensteen made a quick turn to the left and continued the targetless charge through the Flaaghra Tunnels. Samus and Mada narrowly made the turn.

They ran through the caverns with the eerie groaning of the hundred ghosts behind them. The tunnel twisted and turned and ended.

"Why did we stop?" Mada asked.

"It's a dead end," Goldensteen pointed out. The three turned and listened to the shrieks getting louder and louder.

"They're here." Samus stated. She still had her x-ray visor engaged and staring at the wall of ghosts before them. "Goldensteen, isn't there something we can do?"

"I'm trying to remember!" Goldensteen closed his eyes, seemingly falling asleep.

"Goldensteen! This is no time to sleep!" yelled Mada.

"I wasn't sleeping, I was meditating."

"Oh, I'm sure we have time for that!" Mada said, sarcastically.

"We do if it has to do with how we will get out of this situation!" Goldensteen moved to beside Samus. "If I remember correctly, they are particularly susceptible to a concentrated sonic blast."

"I think I could help there." Samus pointed her arm cannon at the ghost wall and engaged her annihilator beam. As she fired, the shrieks became more devastating as one by one, the ghosts disintegrated into nothingness. When a hole big enough for the three to run through was formed, Samus stopped firing and ran through the ghosts. Mada and Goldensteen were close behind. The cold dead fingers of the chozo ghosts reached out and tried to grab them as they passed, but failed.

"Which way?" Samus asked once they reached the main corridor again.

"Go left then take the first right!" They knew the ghosts would quickly regroup, so they had to be quick. The first right came up quickly and once again, Samus nearly missed it. This tunnel was not as long, but there was a strange machine at the end.

"I trust you know how to operate the device, Goldensteen?" asked Mada when they approached the apparatus.

"Yes. This is it. The transport to the Phazon Mines." Goldensteen stepped forward and placed his hand on a panel just off the right side of the tunnel. A small hologram formed on the transport. "Now, just stand in the hologram and you shall be on your way."

"Aren't you coming?" asked Samus.

"No, I am afraid I cannot," Goldensteen denied. "I don't have any means of protecting myself from the space pirates. The ghosts will leave me alone since I am chozo. Trust me. I am more use to you at New Chozodia than at your side."

Samus Aran stepped forth onto the transport soon to be followed by Mada Edoc, who stepped into the hologram. Goldensteen watched as they sank into the ground.


End file.
